2pyu | pdb_00002pyu

Structure of the E. coli inosine triphosphate pyrophosphatase RgdB in complex with IMP

spinqualitylabelsall models 2pyu, resolution 2.02Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 2pyu is a 1 chain structure with sequence from Ecoli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: EDO, IMP Related: 1k7k, 2q16 Gene: yggV (ECOLI) Activity: Nucleoside-triphosphate diphosphatase, with EC number 3.6.1.19 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [RDGB_ECOLI] Pyrophosphatase that hydrolyzes the non-canonical purine nucleotides deoxyinosine triphosphate (dITP) and xanthosine triphosphate (XTP) as well as 2'-deoxy-N-6-hydroxylaminopurine triposphate (dHAPTP) to their respective monophosphate derivatives. Probably excludes non-canonical purines from DNA precursor pool, thus preventing their incorporation into DNA and avoiding chromosomal lesions.[HAMAP-Rule:MF_01405] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMed Inosine triphosphate pyrophosphatases, which are ubiquitous house-cleaning enzymes, hydrolyze noncanonical nucleoside triphosphates (inosine triphosphate (ITP) and xanthosine triphosphate (XTP)) and prevent the incorporation of hypoxanthine or xanthine into nascent DNA or RNA. Here we present the 1.5-A-resolution crystal structure of the inosine triphosphate pyrophosphatase RdgB from Escherichia coli in a free state and in complex with a substrate (ITP+Ca(2+)) or a product (inosine monophosphate (IMP)). ITP binding to RdgB induced a large displacement of the alpha1 helix, closing the enzyme active site. This positions the conserved Lys13 close to the bridging oxygen between the alpha- and beta-phosphates of the substrate, weakening the P(alpha)-O bond. On the other side of the substrate, the conserved Asp69 is proposed to act as a base coordinating the catalytic water molecule. Our data provide insight into the molecular mechanisms of the substrate selectivity and catalysis of RdgB and other ITPases. Molecular basis of the antimutagenic activity of the house-cleaning inosine triphosphate pyrophosphatase RdgB from Escherichia coli.,Savchenko A, Proudfoot M, Skarina T, Singer A, Litvinova O, Sanishvili R, Brown G, Chirgadze N, Yakunin AF J Mol Biol. 2007 Dec 7;374(4):1091-103. Epub 2007 Oct 11. PMID:17976651 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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